While the regular 2-D mesh topology has been utilized for most of Network-on-Chips (NoCs) on FPGAs, spatially biased traffic in some applications make some customization method feasible. A link removal strategy that customizes the router in NoC is proposed for reconfigurable systems in order to minimize required hardware amount. Based on the pre-analyzed traffic information, links on which the communication amount is small are removed to reduce the hardware cost with enough performance being kept. Two policies are proposed to avoid deadlocks and better performance can be achieved compared with up*/down* routing on the irregular topology with links removed. In the image recognition application susan, the proposed method can save 30% of the hardware amount without performance degradation.